Recent sequencing techniques allow the simultaneous determination of large quantities of nucleotide sequences. Typically, a DNA or RNA target sample is fragmented by mechanical or enzymatic techniques, after which individual fragments are bound to a substrate (e.g. the wall of a reaction chamber, a microarray or a microcarrier/bead) via a nucleotide linker molecule that is attached to the substrate and that is able to capture a fragment. For technologies other than single molecule sequencing, a PCR-based amplification step follows. Subsequently, nucleotides are stepwise incorporated and identified for each DNA or RNA fragment bound to the substrate. This process is repeated a number of times and the sequencing reads of all the individual fragments are aligned to get the complete sequence of the target sample under investigation.
Currently, targeted resequencing is developing into the standard procedure within the sequencing field, as this may enable one to focus the sequencing on those sections of the DNA that may be clinically relevant. In target sequencing, specific fragments of the target sample are captured by specific capture probes. Although this may be advantageous as it may save sequencing costs, the bioinformatics analysis may be still a very laborious process which takes easily a week for most analyses.
In WO 2010/097775 A1 a capture oligonucleotide probe is attached to an encoded microcarrier, wherein the code of the microcarrier identifies the sequence of the oligonucleotide probe. After the sequence determination, the nucleotide sequence of the capture oligonucleotide probe is identified by determining the code on the microcarrier.